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Technical documentation
Nic Hannah edited this page Oct 4, 2018
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is here: MOM_diags.txt (best viewed as "raw").
A comprehensive tabulation of MOM diagnostics does not exist.
A set of Unix commands to generate such a list is offered on p.413 of S. M. Griffies "Elements of the Modular Ocean Model (MOM) 5 (2012 release with updates)" [Technical Report 7, NOAA/Geophysical Fluid Dynamics Laboratory Ocean Group, February 2012] but this does not deal well with diagnostic registrations that span multiple lines.
The list offered here is more complete, but not without its own problems. Hopefully it will be of some use.
This is a work in progress.
Some of these diags may not actually be available because the functions may not be called.
Also many names are programmatically generated so you have to dive into the code to figure out what they are, eg
e: id_yflux_adv_int_z ( n ) = register_diag_field ( 'ocean_model' , trim ( t_prog ( n ) % name ) // '_yflux_adv_int_z' , grd % tracer_axes_flux_y ( 1 : 2 ) , time % model_time , 'z-integral of cp*rho*dxt*v*temp' , 'Watts' , missing_value = missing_value , range = ( / - 1.e18 , 1.e18 / ) )
(we are working on dealing with that case)
The diag list was produced by Marshall Ward using flint to parse the entire MOM codebase via this script (named parse.py):
from flint.project import Project
proj = Project(verbose=True)
proj.parse('mom5/mom5')
The parse.py script was run (python works find if 3.x is installed):
python3 parse.py > out
The parsed output out is then filtered with grep to just list the lines with diag_table field registrations:
grep -e "^mom5" -e "= *register_diag_field" out > MOM_diags.txt
This page records the timestep sequence found to successfully spin up various configurations of ACCESS-OM2 and related models.
These can be updated via (for example)
cd /g/data3/hh5/tmp/cosima/access-om2-025/025deg_jra55_ryf_spinup7
echo "## $PWD"; echo -e '| run | years | months | days | timestep |\n| --- | --- | --- | --- | --- |'; for file in output*; do echo -n "| $file |"; grep -m 1 -A 2 years: "$file"/config.yaml | tr -s '\n' '| '; grep -m 1 timestep: "$file"/config.yaml | tr -s '\n' ' '; echo '|'; done| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output001 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output001 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output002 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output003 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output004 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output005 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output006 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output007 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output008 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output009 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output010 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output011 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output012 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output013 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output014 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output015 | years: 0 | months: 1 | days: 0 | timestep: 240 |
| output016 | years: 0 | months: 1 | days: 0 | timestep: 240 |
| output017 | years: 0 | months: 1 | days: 0 | timestep: 240 |
| output018 | years: 0 | months: 1 | days: 0 | timestep: 240 |
| output019 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output020 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output021 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output022 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output023 | years: 0 | months: 1 | days: 0 | timestep: 240 |
| output024 | years: 0 | months: 1 | days: 0 | timestep: 240 |
| output025 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output026 | years: 0 | months: 2 | days: 0 | timestep: 300 |
| output027 | years: 0 | months: 2 | days: 0 | timestep: 450 |
| output028 | years: 0 | months: 2 | days: 0 | timestep: 450 |
| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 1 | months: 0 | days: 0 | timestep: 600 |
| output001 | years: 1 | months: 0 | days: 0 | timestep: 600 |
| output002 | years: 1 | months: 0 | days: 0 | timestep: 900 |
| output003 | years: 1 | months: 0 | days: 0 | timestep: 900 |
| output004 | years: 1 | months: 0 | days: 0 | timestep: 1350 |
| output005 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output006 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output007 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output001 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output002 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output003 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output004 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output005 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output001 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output002 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output003 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output004 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output005 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output006 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output007 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output008 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output009 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output010 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output011 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output012 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output013 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output014 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output015 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output016 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output017 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output018 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output019 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output020 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output021 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output022 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output023 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output024 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output025 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output026 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output027 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output028 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output029 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output030 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output031 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output032 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output033 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output034 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output035 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output036 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output037 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output038 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output039 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output040 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output041 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output042 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output043 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output044 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output045 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output046 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output047 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output048 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output049 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output050 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output051 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output052 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output053 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output054 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output055 | years: 2 | months: 0 | days: 0 | timestep: 3600 |
| output056 | years: 2 | months: 0 | days: 0 | timestep: 5400 |
| output057 | years: 2 | months: 0 | days: 0 | timestep: 5400 |
| output058 | years: 2 | months: 0 | days: 0 | timestep: 5400 |
| output059 | years: 2 | months: 0 | days: 0 | timestep: 5400 |
| output060 | years: 2 | months: 0 | days: 0 | timestep: 5400 |
| output061 | years: 2 | months: 0 | days: 0 | timestep: 5400 |
| output062 | years: 2 | months: 0 | days: 0 | timestep: 5400 |
| run | years | months | days | timestep |
|---|---|---|---|---|
| output000 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output001 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output002 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output003 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output004 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output005 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output006 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output007 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output008 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output009 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output010 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output011 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output012 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output013 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output014 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output015 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output016 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output017 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output018 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output019 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output020 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output021 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output022 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output023 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output024 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output025 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output026 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output027 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output028 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output029 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output030 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output031 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output032 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output033 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output034 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output035 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output036 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output037 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output038 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output039 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output040 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output041 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output042 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output043 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output044 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output045 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output046 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output047 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output048 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output049 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output050 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output051 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output052 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output053 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output054 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output055 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output056 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output057 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output058 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output059 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output060 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output061 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output062 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output063 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output064 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
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| output070 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output071 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output072 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output073 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
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| output092 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output093 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output094 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output095 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output096 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
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| output112 | years: 1 | months: 0 | days: 0 | timestep: 1800 |
| output113 | years: 1 | months: 0 | days: 0 | timestep: 3600 |
| output114 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output115 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output116 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output117 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output118 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output119 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output120 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output121 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output122 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output123 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output124 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
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| output190 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output191 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output192 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output193 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output194 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output195 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output196 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output197 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output198 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output199 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output200 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output201 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output202 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output203 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output204 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output205 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output206 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output207 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output208 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output209 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output210 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output211 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output212 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output213 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output214 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output215 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output216 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output217 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output218 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output219 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output220 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output221 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output222 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output223 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output224 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
| output225 | years: 1 | months: 0 | days: 0 | timestep: 5400 |
- Quick start
- Downloading ACCESS-OM2
- Building the models
- Running a test case
- Checking model output
- Running on gadi
- Updating an experiment
- Creating a new experiment
- Starting an experiment from existing restarts
- Integrating with the COSIMA cookbook
- Archiving model output
- Updating model bathymetry
- Perturbing the forcing fields
- Changing the bathymetry, land-sea mask and OASIS remapping weights
- Overview
- Coupling strategy
- Model load balancing
- CICE block distribution
- Build system
- Future work
- libaccessom2 / YATM
- MOM
- CICE
- Building models individually
- Installing new executables
- Contributing changes to the ACCESS-OM2 repository
- Testing
- Release history